Contacts of the helix formed by residues 709 - 720 (chain V) in PDB entry 1I84
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 709 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490V GLN* 4.3 0.2 - - - +
493V PHE* 4.0 8.4 - - - -
498V PHE* 4.2 0.7 - - - -
519V LEU* 4.0 16.6 - - - +
706V ARG 3.4 10.9 + - - -
707V CYS 3.5 0.8 - - - -
708V ASN* 1.3 79.9 - - - +
710V VAL* 1.3 52.5 + - - +
712V GLU* 2.8 24.9 - - - +
713V GLY* 2.7 34.0 + - - -
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Residues in contact with VAL 710 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89V MET* 5.9 0.4 - - + -
100V VAL* 4.6 7.6 - - + -
117V SER* 4.4 4.7 - - - -
120V PHE* 3.4 24.3 - - + -
122V VAL* 4.6 10.1 - - + -
683V ARG* 5.4 6.3 - - + -
685V ILE* 5.3 1.6 - - + -
705V LEU* 3.5 48.9 + - + +
708V ASN* 3.4 12.3 - - + +
709V GLY* 1.3 73.5 - - - +
711V LEU* 1.3 74.8 - - + +
712V GLU* 3.5 0.2 + - - -
713V GLY* 2.7 13.5 + - - -
714V ILE* 3.0 27.8 + - + +
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Residues in contact with LEU 711 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95V LEU* 3.8 16.0 - - + +
96V ASN* 3.7 18.8 - - - +
97V GLU* 4.7 14.6 - - + +
100V VAL* 3.3 42.2 - - + -
705V LEU* 3.9 22.0 - - + +
706V ARG* 6.4 0.4 - - + -
710V VAL* 1.3 75.9 - - + +
712V GLU* 1.3 62.9 + - + +
714V ILE* 2.6 29.5 + - - +
715V ARG* 2.9 15.7 + - + +
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Residues in contact with GLU 712 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498V PHE* 3.3 28.0 - - + -
517V PHE* 3.6 30.7 - - + +
519V LEU* 4.0 14.0 - - + +
705V LEU 5.1 0.9 - - - +
706V ARG* 4.6 7.3 - - - +
709V GLY* 2.8 32.8 - - - +
711V LEU* 1.3 71.9 + - + +
713V GLY* 1.3 53.2 + - - +
714V ILE 2.7 15.6 + - - -
715V ARG* 2.9 18.1 + - - +
716V ILE* 3.5 9.2 + - - +
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Residues in contact with GLY 713 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120V PHE* 3.0 28.4 - - - -
493V PHE* 4.4 0.7 - - - -
497V MET* 4.3 10.4 - - - +
498V PHE* 3.7 12.0 - - - -
709V GLY 2.7 17.2 + - - -
710V VAL 2.7 8.0 + - - -
712V GLU* 1.3 75.3 - - - +
714V ILE* 1.3 55.7 + - - +
716V ILE* 4.1 4.6 - - - +
717V CYS* 3.0 17.8 - - - -
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Residues in contact with ILE 714 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89V MET* 4.2 13.9 - - + -
90V ALA* 3.7 30.3 - - + -
95V LEU* 3.8 27.1 - - + -
100V VAL* 5.1 4.0 - - + -
117V SER* 3.4 44.0 - - - -
120V PHE* 4.0 0.2 - - + -
710V VAL* 3.0 28.1 + - + +
711V LEU* 2.6 20.1 + - - +
713V GLY* 1.3 74.8 - - - +
715V ARG* 1.3 63.8 + - - +
716V ILE 3.3 1.8 - - - -
717V CYS* 3.0 15.6 + - - +
718V ARG* 3.1 10.6 + - + +
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Residues in contact with ARG 715 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95V LEU* 5.1 7.4 - - + -
515V ILE* 4.6 22.9 - - - +
517V PHE* 3.8 18.7 - - + -
711V LEU* 2.9 12.6 + - + +
712V GLU* 2.9 12.4 + - - +
714V ILE* 1.3 75.8 - - - +
716V ILE* 1.3 51.5 + - - +
718V ARG* 2.9 27.9 + - - +
719V GLN* 2.3 82.7 + - - +
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Residues in contact with ILE 716 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V LEU* 5.3 1.8 - - + -
497V MET* 4.1 24.5 - - + +
498V PHE* 5.1 2.7 - - + -
501V GLU* 4.2 21.3 - - + +
502V GLN* 5.2 4.0 - - - +
505V TYR* 4.2 9.2 - - + +
512V TRP* 3.7 26.0 - - + -
517V PHE* 4.2 22.1 - - + -
712V GLU 3.5 5.8 + - - +
713V GLY* 4.1 16.8 - - - +
715V ARG* 1.3 80.1 - - - +
717V CYS* 1.3 68.0 + - - +
719V GLN* 3.8 4.5 - - + -
720V GLY* 2.6 46.4 + - - +
722V PRO* 4.1 3.4 - - + +
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Residues in contact with CYS 717 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90V ALA* 4.8 6.7 - - + -
118V GLY* 3.6 28.9 - - - -
119V LEU* 3.5 30.1 - - + -
713V GLY 3.0 28.7 - - - -
714V ILE 3.0 8.3 + - - +
716V ILE* 1.3 83.7 - - - +
718V ARG* 1.3 59.9 + - - +
720V GLY 4.0 1.0 - - - +
722V PRO* 3.7 19.4 - - + +
777V ARG* 5.5 0.3 - - - +
778V THR* 3.0 30.0 + - + +
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Residues in contact with ARG 718 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90V ALA* 5.1 11.9 - - + +
95V LEU* 3.6 33.2 - - + +
714V ILE* 3.1 8.7 + - + +
715V ARG* 2.9 31.6 + - - +
717V CYS* 1.3 78.6 - - + +
719V GLN* 1.3 93.5 + - + +
720V GLY 3.9 1.2 - - - +
777V ARG* 3.8 13.0 + - - +
778V THR* 5.0 0.9 - - - -
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Residues in contact with GLN 719 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512V TRP* 4.2 12.4 - - + -
515V ILE* 5.9 3.3 - - + +
517V PHE* 5.4 3.8 - - + -
715V ARG* 2.3 91.5 + - + +
716V ILE* 3.8 7.6 - - + +
718V ARG* 1.3 91.3 + - + +
720V GLY* 1.3 55.6 + - - +
721V PHE* 4.2 2.8 - - - -
777V ARG* 2.8 26.5 + - - -
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Residues in contact with GLY 720 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505V TYR* 3.8 1.3 - - - -
512V TRP* 3.7 14.1 - - - -
716V ILE* 2.6 28.3 + - - +
717V CYS 4.0 1.4 - - - +
718V ARG 3.9 2.9 - - - +
719V GLN* 1.3 78.0 - - - +
721V PHE* 1.3 72.6 + - - -
722V PRO* 3.3 12.9 - - - +
777V ARG* 3.4 13.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il